| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 272 |
| Agnébi | River (basin) | native | 272 |
| Aruwimi River | River (basin) | native | 106290 |
| Bandama | River (basin) | native | 272 |
| Bandama | River (basin) | native | 272 |
| Benue River | River (basin) | native | 13331 |
| Benue River | River (basin) | native | 13331 |
| Bia | River (basin) | native | 272 |
| Bia | River (basin) | native | 272 |
| Cavally | River (basin) | native | 13331 |
| Cavally | River (basin) | native | 13331 |
| Chad | Lake | native | 3203 |
| Comoé | River (basin) | native | 272 |
| Comoé | River (basin) | native | 272 |
| Congo | River (basin) | native | 367 |
| Congo | River (basin) | native | 42505 |
| Cross | River (basin) | native | 13331 |
| Cross | River (basin) | native | 13331 |
| Ébrié Lagoon | Lagoon | native | 28587 |
| Ébrié Lagoon | Lagoon | native | 28587 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Gambia | River (basin) | native | 3203 |
| Gambia | River (basin) | native | 3203 |
| Géba | River (basin) | native | 13331 |
| Géba | River (basin) | native | 13331 |
| Kainji Lake | Lake | native | 28265 |
| Kainji Lake | Lake | native | 28265 |
| Kasai River | River (basin) | native | 42505 |
| Lindi-Tshopo Region | River (basin) | questionable | 42505 |
| Lualaba | River (basin) | native | 42505 |
| Malebo Pool | Lake | native | 42505 |
| Middle Congo | River (basin) | native | 42505 |
| Mono | River (basin) | native | 13331 |
| Mono | River (basin) | native | 13331 |
| Niger | River (basin) | native | 3203 |
| Niger | River (basin) | native | 3203 |
| Ogun | River (basin) | native | 13331 |
| Ogun | River (basin) | native | 13331 |
| Ouémé | River (basin) | native | 13331 |
| Ouémé | River (basin) | native | 13331 |
| Ruki River Region | River (basin) | native | 42505 |
| Sanaga | River (basin) | native | 51193 |
| Sanaga | River (basin) | native | 51193 |
| Sangha | River (basin) | native | 44840 |
| Sankuru | River (basin) | native | 42505 |
| Sassandra | River (basin) | native | 272 |
| Sassandra | River (basin) | native | 272 |
| Senegal | River (basin) | native | 3203 |
| Senegal | River (basin) | native | 3203 |
| Tano | River (basin) | native | 13331 |
| Tano | River (basin) | native | 13331 |
| Ubangui | River (basin) | native | 42505 |
| Uélé | River (basin) | native | 42505 |
| Upper Lualaba | River (basin) | native | 42505 |
| Volta | Lake | native | 3203 |
| Wagenia Falls | River (basin) | native | 106245 |